The human genome ten years on (part 2) – it ain’t necessarily so

June 14, 2010 • 11:14 am

by Greg Mayer

In a post a couple of months ago, Matthew took note of the tenth anniversary of the completion of the draft human genome, noting that Nature had published a retrospective.  Matthew rightfully took issue with the dreadful “blueprint” metaphor for the genome, but also concisely noted the meager medical results:

…despite all the hype, the contribution of the genome to human health has been pretty negligible. In other words, from a purely medical point of view, there isn’t much to celebrate.

In yesterday’s New York Times, Nicholas Wade provides a journalistic analysis, and confirms that the results so far are disappointing. Money quote:

…the primary goal of the $3 billion Human Genome Project — to ferret out the genetic roots of common diseases like cancer and Alzheimer’s and then generate treatments — remains largely elusive. Indeed, after 10 years of effort, geneticists are almost back to square one in knowing where to look for the roots of common disease.

This does not come as much of a surprise when you realize that most diseases are not genetically caused (in any straightforward reading of the word caused); that even when there is a genetic basis, the genetics are apt to be complex; and that even when simple, identification of a gene does not lead readily to a cure. These issues were raised most presciently by Dick Lewontin, especially in an essay-review (subscription required) he wrote for The New York Review of Books in 1992. Dick decried scientists’ selling the genome project to governments on the basis of its health benefits, while in fact the project would primarily advance disciplinary (and, in some cases, financial) interests. Endorsing Dick’s genetic arguments, I wrote the following in 2000, at the time of the announcement by Bill Clinton and Tony Blair:

Few diseases are caused by a “gene.” Most diseases, in fact, are caused by the invasion of the body by another organism (bacteria, viruses, protozoa). Our susceptibility and resistance to disease may often have a genetic basis, but these too are usually the result of multiple genes in interaction with the environment. Even when a disease does have a singular genetic cause, finding the gene does not necessarily lead easily to treatment or prevention (e.g. cystic fibrosis).

Last year, over at Mermaid’s Tale (in a post I noted here at WEIT), Ken Weiss put it succinctly (he also discusses Wade’s new NYT article here):

…most common diseases have little to do with genetic variation in any sensible way.

The genome project has provided much useful scientific information. As Wade notes, “For biologists, the genome has yielded one insightful surprise after another.” But that’s not why the project was done. Bill Clinton said it would lead to treatments for “most, if not all, human diseases”; Francis Collins said we’d have genetic diagnosis of diseases within ten years. The genome project’s architects oversold it’s medical (not to mention philosophical) benefits, and now scientists (or at least genome scientists) will lose credibility because of it. Harold Varmus is quoted by Wade as saying “Genomics is a way to do science, not medicine.” If only that had been said louder, and earlier, and by more people.

[PZ and some others are taking Wade to task for saying “humans… [are] higher on the evolutionary scale”. While this is an inopportune use of the scala naturae, it’s part of one paragraph (which does make the interesting point that genome size, as measured by number of protein coding genes, does not vary very widely among metazoans), and does not detract at all from the main thrust of the article.]

Philip Kitcher on science journalism

June 3, 2010 • 12:48 pm

by Greg Mayer

In tomorrow’s issue of Science, the distinguished philosopher of science Philip Kitcher reviews several books on climate change (pre-publication version here).  He has written a great deal about creationism (most notably in the classic Abusing Science and the more recent Living with Darwin), and so it is natural that he would come to be interested in the issues surrounding scientific knowledge, public debate, and decision-making in democracies. He has written most extensively about these issues in Science, Truth, and Democracy, and he examines them in his review as they relate to several recent books on climate change.

WEIT readers will want to read the whole of Philip’s essay-review for what he has to say about the climate change debate, and his clarification of the different questions involved: is there anthropogenic warming (yes), what are the consequences (diverse and often bad, but of varying certainty as to their eventuality), and what is to be done (the most difficult; bottom line on doubters of change and consequences: “Tell it to the Maldives!”). Of most immediate interest to WEIT though is what he has to say about media coverage, seen in this case from the perspective of a scientific discipline rather different from evolutionary biology (although the opponents of science seem to be in part the same people). He decries the “he said, she said” format beloved of most American news media.

[the] web of connections among aging scientists, conservative politicians, and executives of companies (particularly those involved in fossil fuels) with a short-term economic interest in denying the impact of the emission of carbon into the atmosphere….could not have produced the broad public skepticism about climate change without help from the media. As Oreskes and Conway point out, “balanced coverage” has become the norm in the dissemination of scientific information. Pitting adversaries against one another for a few minutes has proven an appealing strategy for television news programs to pursue in attracting and retaining viewers. Nor is the idea of “fair and balanced” coverage, in which the viewer (or reader) is allowed to decide, confined to Fox News. Competing “experts” have become common on almost all American radio and television programs, the Internet is awash in adversarial exchanges among those who claim to know, and newspapers, too, “sell” science by framing it as a sport (preferably as much of a contact sport as possible). Oreskes and Conway identify the ways in which the Washington Times and the Wall Street Journal have nourished the public sense that anthropogenic climate change is a matter of dispute, how they have given disproportionately large space to articles and opinion pieces from the “merchants of doubt,” and how they have sometimes censored the attempts of serious climate scientists to set the record straight. Even the New York Times, the American newspaper that takes science reporting most seriously, typically “markets” scientific research by imposing a narrative based on competition among dissenting scientists.

This tendency to “he said, she said” journalism has been noted before here at WEIT, and we have happily noted exceptions.

“Oriental yeti”– April Fools?

April 5, 2010 • 11:30 pm

by Greg Mayer

The Telegraph and the Times have stories up about the creature below from China, which they’ve dubbed the “oriental yeti”.

"Oriental yeti" from the Telegraph.

The Times headline writer notes that it “looks like a bear without fur”. The story is so absurd, I first thought it an April Fools joke, but the datelines are April 5 or 6, so I guess not.

So what’s absurd? First, there’s the name. ‘Yeti’ is a name for the abominable snowman, the supposed bipedal ape or ape-man of the Himalayas. The animal in the photo obviously bears not the slightest resemblance to a man or ape. ‘Oriental’ is a curious modifier for yeti, since yetis are Oriental– they occur (or are supposed to occur) in Asia. Whoever bestowed this moniker on the creature evidently hasn’t the slightest idea what the word ‘yeti’ means, and perhaps doesn’t know what ‘oriental’ means either.

Then there’s the description of it as a ‘bear without fur’. While it is only very sparsely haired, it doesn’t look at all like a bear. The head and ear shape are all wrong, but if this is too subtle, it has a long, thick tail! (Hint: bears have very short tails; more bear info here.) The creature is said to have emerged from ‘ancient woodlands’, which sounds mysterious, but the articles note it was trapped by local hunters. Both articles betray very low standards of science journalism; really, in fact, no standards at all.

So it’s not a bear or a yeti; what is it? It’s clearly a mammal of the order Carnivora (but not of the bear family, Ursidae) suffering from some skin disease, likely mange. It doesn’t look like a member of the dog, cat or weasel families to me, but it does look like a civet, so my money is on a mangy civet. (Here’s info on a civet that occurs in China– I’m not saying it’s this particular species; more on civets in general here.) The forlorn looking critter is said to have been sent to Beijing for DNA tests. Darren Naish over at Tetrapod Zoology is good at getting to the bottom of these sorts of stories, and I hope he’ll take this one up.

By the way, this is what a mangy bear does look like.

Mangy American black bear from

UPDATE. At Mammoth Tales, John McKay also says it’s a civet, specifically a binturong.

Pseudoscientist reprimanded, pseudoscience retracted

February 4, 2010 • 1:20 pm

by Greg Mayer

Following up on a comment by Glen Davidson to my latest dowsing post, in which he noted that the UK’s General Medical Council had ruled against anti-vaccination activist Dr. Andrew Wakefield, finding him callous, unethical and dishonest, I note that The Lancet (registration required) has retracted Wakefield and coauthors’ 1998 paper that set off the autism/vaccination controversy. The editors of The Lancet now accept that not only should the paper not have been published, but that its conclusions are false.

The NY Times also covered the story, in a manner I found refreshing. Too often, perhaps due to some distorted sense of objectivity, news reporting consists of a “he said, she said” style, in which opposing viewpoints are given equal status, regardless of the plausibility or support for the claims made.  You’ve all read the kind of story that will have a line like, “Dr. Smith, a paleontologist at the natural history museum, said Triceratops had been extinct for more than 60 million years before the origin of man, while Dr. Jones from the institute said Triceratops had been ridden by men like horses until the recent worldwide flood drowned them all”. The Times reporter, Gardiner Harris, however is familiar with the evidence.

After Dr. Wakefield’s study, vaccination rates plunged in Britain and the number of measles cases soared.

In the United States, anti-vaccine groups have advanced other theories since then to explain why they think vaccines cause autism. For years, they blamed thimerosal, a vaccine preservative containing mercury. Because of concerns over the preservative, vaccine makers in 2001 largely eliminated thimerosal from routinely administered childhood vaccines.

But this change has had no apparent impact on childhood autism rates. Anti-vaccine groups now suggest that a significant number of children have a cellular disorder whose effects are set off by vaccinations.

With each new theory, parents’ groups have called for research to explore possible links between vaccination and autism. Study after study has failed to show any link, and prominent scientific agencies have concluded that scarce research dollars should be spent investigating other possible causes of autism.

(I’ll add parenthetically that I find the notion of “retracting” a paper silly.  Once it’s published, it can’t be unpublished. But it is proper for editors and/or authors to later publish to say that a paper’s data or conclusions were flawed, unwarranted, or false.)